noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.4.1.3.4) Plots of Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'.

Plots are shown with relation to various combinations of meta data variables and in different graphical representations. Lots of plots here.

(1.4.1.3.4.2) Iterating over all combinations of grouping variables
(1.4.1.3.4.2.1) Entire pool of samples
(1.4.1.3.4.2.2) Iterating over Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order
(1.4.1.3.4.2.2.1) Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order: GeneSelector paired test ranking
(1.4.1.3.4.2.2.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.4.1.3.4.2.2.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.4.1.3.4.2.2.2.1.1) Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.3.4.2.2.2.1.1.0) Table 250. Data table used for plots. Data for all pooled samples. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.3.4.2.2.2.1.1.0-323346c6a64.1.4.1.3.4.2.2.2.1.1.csv

.record.id feature abundance.diff
SB11 Bacteroides 1.903e-02
SB16 Bacteroides 9.200e-02
SB18 Bacteroides 5.594e-01
SB28 Bacteroides 1.542e-01
SB29 Bacteroides 5.088e-01
SB34 Bacteroides -1.617e-02
SB36 Bacteroides 1.953e-01
SB39 Bacteroides -1.713e-01
SB4 Bacteroides -3.877e-02
SB41 Bacteroides 7.259e-03
SB43 Bacteroides 3.308e-02
SB44 Bacteroides 7.456e-01
SB5 Bacteroides -3.611e-02
SB9 Bacteroides 1.383e-02
SB11 Prevotella 1.074e-02
SB16 Prevotella 3.024e-04
SB18 Prevotella -2.066e-03
SB28 Prevotella 0.000e+00
SB29 Prevotella 3.600e-04
SB34 Prevotella 8.926e-05
SB36 Prevotella -2.667e-01
SB39 Prevotella -1.127e-04
SB4 Prevotella -1.028e-04
SB41 Prevotella -2.149e-04
SB43 Prevotella 3.917e-01
SB44 Prevotella -3.103e-04
SB5 Prevotella -6.267e-01
SB9 Prevotella -5.996e-01
SB11 Parabacteroides -1.029e-01
SB16 Parabacteroides -1.670e-04
SB18 Parabacteroides -4.008e-04
SB28 Parabacteroides -1.692e-01
SB29 Parabacteroides 6.370e-03
SB34 Parabacteroides 0.000e+00
SB36 Parabacteroides 4.136e-02
SB39 Parabacteroides -4.373e-05
SB4 Parabacteroides -2.569e-04
SB41 Parabacteroides 1.497e-04
SB43 Parabacteroides 5.509e-02
SB44 Parabacteroides 0.000e+00
SB5 Parabacteroides -2.807e-04
SB9 Parabacteroides 3.829e-04
SB11 Faecalibacterium -1.125e-02
SB16 Faecalibacterium -7.158e-03
SB18 Faecalibacterium -3.502e-01
SB28 Faecalibacterium -1.501e-02
SB29 Faecalibacterium 8.999e-03
SB34 Faecalibacterium 5.444e-03
SB36 Faecalibacterium 2.635e-02
SB39 Faecalibacterium -3.989e-02
SB4 Faecalibacterium 9.151e-03
SB41 Faecalibacterium -2.501e-02
SB43 Faecalibacterium 2.918e-02
SB44 Faecalibacterium -3.242e-01
SB5 Faecalibacterium 1.145e-01
SB9 Faecalibacterium 8.209e-03
SB11 Unclassified_Lachnospiraceae -2.678e-02
SB16 Unclassified_Lachnospiraceae 1.918e-02
SB18 Unclassified_Lachnospiraceae -9.434e-02
SB28 Unclassified_Lachnospiraceae -3.522e-02
SB29 Unclassified_Lachnospiraceae 2.825e-03
SB34 Unclassified_Lachnospiraceae 1.867e-02
SB36 Unclassified_Lachnospiraceae -5.679e-02
SB39 Unclassified_Lachnospiraceae -1.802e-02
SB4 Unclassified_Lachnospiraceae 5.201e-03
SB41 Unclassified_Lachnospiraceae 6.086e-03
SB43 Unclassified_Lachnospiraceae -1.535e-01
SB44 Unclassified_Lachnospiraceae -1.796e-01
SB5 Unclassified_Lachnospiraceae 7.834e-02
SB9 Unclassified_Lachnospiraceae 4.273e-02
SB11 Lactobacillus 0.000e+00
SB16 Lactobacillus -5.567e-05
SB18 Lactobacillus 6.199e-04
SB28 Lactobacillus 0.000e+00
SB29 Lactobacillus 0.000e+00
SB34 Lactobacillus 0.000e+00
SB36 Lactobacillus 0.000e+00
SB39 Lactobacillus 0.000e+00
SB4 Lactobacillus 0.000e+00
SB41 Lactobacillus 0.000e+00
SB43 Lactobacillus -1.018e-03
SB44 Lactobacillus -3.103e-04
SB5 Lactobacillus 1.961e-03
SB9 Lactobacillus 4.491e-03
SB11 Enterococcus 0.000e+00
SB16 Enterococcus 0.000e+00
SB18 Enterococcus 7.126e-02
SB28 Enterococcus 3.934e-04
SB29 Enterococcus -6.612e-01
SB34 Enterococcus -8.525e-05
SB36 Enterococcus 0.000e+00
SB39 Enterococcus 0.000e+00
SB4 Enterococcus -1.777e-04
SB41 Enterococcus 0.000e+00
SB43 Enterococcus -6.788e-04
SB44 Enterococcus 0.000e+00
SB5 Enterococcus 1.089e-04
SB9 Enterococcus 7.573e-04
SB11 Alistipes 2.004e-01
SB16 Alistipes -1.674e-01
SB18 Alistipes 2.480e-04
SB28 Alistipes 0.000e+00
SB29 Alistipes 2.807e-02
SB34 Alistipes -3.394e-02
SB36 Alistipes 2.739e-02
SB39 Alistipes -4.407e-03
SB4 Alistipes 0.000e+00
SB41 Alistipes 1.169e-02
SB43 Alistipes 1.058e-02
SB44 Alistipes 4.393e-03
SB5 Alistipes -6.851e-04
SB9 Alistipes 0.000e+00
SB11 Lachnospiracea_incertae_sedis -2.726e-02
SB16 Lachnospiracea_incertae_sedis -3.510e-03
SB18 Lachnospiracea_incertae_sedis -5.343e-02
SB28 Lachnospiracea_incertae_sedis -5.969e-02
SB29 Lachnospiracea_incertae_sedis 3.240e-03
SB34 Lachnospiracea_incertae_sedis -1.643e-02
SB36 Lachnospiracea_incertae_sedis -2.874e-02
SB39 Lachnospiracea_incertae_sedis -5.941e-03
SB4 Lachnospiracea_incertae_sedis 6.921e-04
SB41 Lachnospiracea_incertae_sedis -5.300e-03
SB43 Lachnospiracea_incertae_sedis -1.407e-01
SB44 Lachnospiracea_incertae_sedis -1.205e-01
SB5 Lachnospiracea_incertae_sedis 4.237e-03
SB9 Lachnospiracea_incertae_sedis -8.762e-03
SB11 Clostridium_XI 3.446e-02
SB16 Clostridium_XI -2.186e-03
SB18 Clostridium_XI -1.666e-02
SB28 Clostridium_XI 3.236e-02
SB29 Clostridium_XI 1.800e-03
SB34 Clostridium_XI 5.249e-04
SB36 Clostridium_XI 2.747e-03
SB39 Clostridium_XI 6.716e-03
SB4 Clostridium_XI -1.096e-04
SB41 Clostridium_XI -1.082e-03
SB43 Clostridium_XI -1.461e-01
SB44 Clostridium_XI 2.282e-03
SB5 Clostridium_XI 2.127e-01
SB9 Clostridium_XI 3.483e-02
SB11 Blautia -7.727e-02
SB16 Blautia -1.041e-03
SB18 Blautia -3.563e-02
SB28 Blautia -3.264e-04
SB29 Blautia 1.080e-03
SB34 Blautia 2.461e-02
SB36 Blautia -1.504e-02
SB39 Blautia -8.720e-03
SB4 Blautia 6.934e-03
SB41 Blautia -6.399e-03
SB43 Blautia -1.208e-01
SB44 Blautia -2.787e-03
SB5 Blautia 4.988e-02
SB9 Blautia 4.537e-02
SB11 Erysipelotrichaceae_incertae_sedis -4.125e-04
SB16 Erysipelotrichaceae_incertae_sedis 3.883e-03
SB18 Erysipelotrichaceae_incertae_sedis -1.880e-03
SB28 Erysipelotrichaceae_incertae_sedis 1.416e-03
SB29 Erysipelotrichaceae_incertae_sedis -6.221e-03
SB34 Erysipelotrichaceae_incertae_sedis 7.007e-04
SB36 Erysipelotrichaceae_incertae_sedis -2.877e-04
SB39 Erysipelotrichaceae_incertae_sedis 6.482e-03
SB4 Erysipelotrichaceae_incertae_sedis 3.714e-03
SB41 Erysipelotrichaceae_incertae_sedis -6.165e-04
SB43 Erysipelotrichaceae_incertae_sedis 1.521e-03
SB44 Erysipelotrichaceae_incertae_sedis 7.523e-04
SB5 Erysipelotrichaceae_incertae_sedis 3.499e-02
SB9 Erysipelotrichaceae_incertae_sedis 3.765e-01
SB11 Roseburia -2.166e-02
SB16 Roseburia 6.445e-05
SB18 Roseburia -9.067e-02
SB28 Roseburia -4.079e-02
SB29 Roseburia 3.052e-04
SB34 Roseburia -2.465e-03
SB36 Roseburia -4.243e-03
SB39 Roseburia -1.960e-02
SB4 Roseburia 1.751e-03
SB41 Roseburia 3.222e-03
SB43 Roseburia -1.403e-02
SB44 Roseburia -4.611e-02
SB5 Roseburia 1.556e-02
SB9 Roseburia 1.548e-02
SB11 Escherichia_Shigella 4.464e-04
SB16 Escherichia_Shigella 1.448e-02
SB18 Escherichia_Shigella 0.000e+00
SB28 Escherichia_Shigella 1.738e-01
SB29 Escherichia_Shigella 0.000e+00
SB34 Escherichia_Shigella -8.525e-05
SB36 Escherichia_Shigella 0.000e+00
SB39 Escherichia_Shigella 0.000e+00
SB4 Escherichia_Shigella 0.000e+00
SB41 Escherichia_Shigella -3.863e-05
SB43 Escherichia_Shigella 0.000e+00
SB44 Escherichia_Shigella 1.098e-03
SB5 Escherichia_Shigella 1.282e-01
SB9 Escherichia_Shigella 2.165e-03
SB11 Unclassified_Clostridiales -8.878e-03
SB16 Unclassified_Clostridiales 6.334e-03
SB18 Unclassified_Clostridiales -6.188e-03
SB28 Unclassified_Clostridiales -1.171e-03

(1.4.1.3.4.2.2.2.1.1.1) Widget 262. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data for all pooled samples. Click to see HTML widget file in full window: ./1.4.1.3.4.2.2.2.1.1.1-3235c8e2f19Dynamic.Pivot.Table.html

(1.4.1.3.4.2.2.2.1.1.1) Widget 263. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data for all pooled samples. Click to see HTML widget file in full window: ./1.4.1.3.4.2.2.2.1.1.1-32349ba0ccaDynamic.Pivot.Table.html

(1.4.1.3.4.2.2.2.1.1.1) Table 251. Summary table. Data for all pooled samples. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.3.4.2.2.2.1.1.1-3231989b477.1.4.1.3.4.2.2.2.1.1.csv

feature mean sd median incidence
Lachnospiracea_incertae_sedis -3.300e-02 4.599e-02 -1.259e-02 0.21429
Unclassified_Bacteria 1.975e-03 3.704e-03 1.525e-03 0.64286
Erysipelotrichaceae_incertae_sedis 3.004e-02 1.002e-01 1.084e-03 0.64286
Clostridium_XlVa 3.617e-03 7.901e-03 2.047e-03 0.71429
Clostridium_XVIII 1.560e-03 5.281e-03 5.686e-04 0.71429
Bacteroides 1.476e-01 2.671e-01 2.605e-02 0.71429
Clostridium_XI 1.159e-02 7.258e-02 2.041e-03 0.64286
Roseburia -1.451e-02 2.860e-02 -3.354e-03 0.42857
Clostridium_IV 1.101e-03 3.246e-03 1.683e-04 0.57143
Unclassified_Clostridiales -3.879e-03 1.240e-02 -1.507e-03 0.42857
Unclassified_Lachnospiraceae -2.794e-02 7.235e-02 -7.599e-03 0.50000
Prevotella -7.804e-02 2.619e-01 -1.077e-04 0.35714
Flavonifractor 2.718e-04 3.791e-03 9.648e-04 0.64286
Blautia -1.001e-02 4.470e-02 -1.914e-03 0.35714
Faecalibacterium -4.078e-02 1.307e-01 -8.567e-04 0.50000
Escherichia_Shigella 2.286e-02 5.515e-02 0.000e+00 0.42857
Unclassified_Bacteroidales -1.405e-04 2.990e-02 9.153e-04 0.57143
Unclassified_Ruminococcaceae 1.077e-03 1.151e-02 4.269e-03 0.57143
Ruminococcus 1.937e-04 1.499e-02 -6.987e-04 0.42857
Unclassified_Firmicutes -2.714e-03 8.047e-03 1.221e-04 0.50000
Dorea 3.481e-03 1.169e-02 -1.719e-04 0.42857
Clostridium_sensu_stricto 3.417e-03 1.111e-02 0.000e+00 0.42857
Parabacteroides -1.214e-02 5.681e-02 -2.187e-05 0.35714
Veillonella -6.760e-03 2.190e-02 -4.196e-05 0.28571
Streptococcus 1.742e-03 7.012e-03 -2.569e-05 0.42857
Alistipes 5.451e-03 7.376e-02 1.240e-04 0.50000
Gemmiger -1.209e-03 3.059e-03 0.000e+00 0.28571
Enterococcus -4.212e-02 1.792e-01 0.000e+00 0.28571
Sutterella 1.605e-03 1.226e-02 0.000e+00 0.35714
Turicibacter -1.629e-03 9.729e-03 0.000e+00 0.35714
Lactobacillus 4.063e-04 1.337e-03 0.000e+00 0.21429
Unclassified_Enterobacteriaceae 3.304e-03 1.163e-02 0.000e+00 0.28571
Akkermansia 1.416e-02 4.670e-02 0.000e+00 0.21429
Unclassified_Lactobacillales 1.035e-02 3.879e-02 0.000e+00 0.14286
Megamonas 7.782e-06 2.912e-05 0.000e+00 0.07143
Odoribacter 1.268e-03 5.257e-03 0.000e+00 0.14286
Unclassified_Burkholderiales -3.452e-03 1.294e-02 0.000e+00 0.07143
Parasutterella -8.769e-04 3.786e-03 0.000e+00 0.07143

(1.4.1.3.4.2.2.2.1.1.1) Figure 774. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar_stacked plot. Image file: plots/32324222fb2.svg.

(1.4.1.3.4.2.2.2.1.1.1) Figure 775. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar (sample mean) plot. Image file: plots/32337e78b2d.svg.

(1.4.1.3.4.2.2.2.1.1.1) Figure 776. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/323322ed2c2.svg.

(1.4.1.3.4.2.2.2.1.1.1) Figure 777. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/323ba04e82.svg.

(1.4.1.3.4.2.2.2.1.2) Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.3.4.2.2.2.1.2.1) Figure 778. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. bar (sample mean) plot. Image file: plots/32369a393b7.svg.

(1.4.1.3.4.2.2.2.1.2.1) Figure 779. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/323681864db.svg.

(1.4.1.3.4.2.2.2.1.2.1) Figure 780. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data for all pooled samples. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/32379a4e204.svg.

(1.4.1.3.4.2.3) Grouping variables Drug.Before.Diet
(1.4.1.3.4.2.4) Iterating over Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order
(1.4.1.3.4.2.4.1) Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. profile sorting order: GeneSelector paired test ranking
(1.4.1.3.4.2.4.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.4.1.3.4.2.4.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.4.1.3.4.2.4.2.1.1) Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.3.4.2.4.2.1.1.0) Table 252. Data table used for plots. Data grouped by Drug.Before.Diet. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.3.4.2.4.2.1.1.0-3237e075505.1.4.1.3.4.2.4.2.1.1.csv

.record.id Drug.Before.Diet feature abundance.diff
SB11 DrugBefore_NO Bacteroides 1.903e-02
SB16 DrugBefore_YES Bacteroides 9.200e-02
SB18 DrugBefore_NO Bacteroides 5.594e-01
SB28 DrugBefore_YES Bacteroides 1.542e-01
SB29 DrugBefore_YES Bacteroides 5.088e-01
SB34 DrugBefore_YES Bacteroides -1.617e-02
SB36 DrugBefore_YES Bacteroides 1.953e-01
SB39 DrugBefore_YES Bacteroides -1.713e-01
SB4 DrugBefore_YES Bacteroides -3.877e-02
SB41 DrugBefore_YES Bacteroides 7.259e-03
SB43 DrugBefore_YES Bacteroides 3.308e-02
SB44 DrugBefore_YES Bacteroides 7.456e-01
SB5 DrugBefore_NO Bacteroides -3.611e-02
SB9 DrugBefore_NO Bacteroides 1.383e-02
SB11 DrugBefore_NO Prevotella 1.074e-02
SB16 DrugBefore_YES Prevotella 3.024e-04
SB18 DrugBefore_NO Prevotella -2.066e-03
SB28 DrugBefore_YES Prevotella 0.000e+00
SB29 DrugBefore_YES Prevotella 3.600e-04
SB34 DrugBefore_YES Prevotella 8.926e-05
SB36 DrugBefore_YES Prevotella -2.667e-01
SB39 DrugBefore_YES Prevotella -1.127e-04
SB4 DrugBefore_YES Prevotella -1.028e-04
SB41 DrugBefore_YES Prevotella -2.149e-04
SB43 DrugBefore_YES Prevotella 3.917e-01
SB44 DrugBefore_YES Prevotella -3.103e-04
SB5 DrugBefore_NO Prevotella -6.267e-01
SB9 DrugBefore_NO Prevotella -5.996e-01
SB11 DrugBefore_NO Parabacteroides -1.029e-01
SB16 DrugBefore_YES Parabacteroides -1.670e-04
SB18 DrugBefore_NO Parabacteroides -4.008e-04
SB28 DrugBefore_YES Parabacteroides -1.692e-01
SB29 DrugBefore_YES Parabacteroides 6.370e-03
SB34 DrugBefore_YES Parabacteroides 0.000e+00
SB36 DrugBefore_YES Parabacteroides 4.136e-02
SB39 DrugBefore_YES Parabacteroides -4.373e-05
SB4 DrugBefore_YES Parabacteroides -2.569e-04
SB41 DrugBefore_YES Parabacteroides 1.497e-04
SB43 DrugBefore_YES Parabacteroides 5.509e-02
SB44 DrugBefore_YES Parabacteroides 0.000e+00
SB5 DrugBefore_NO Parabacteroides -2.807e-04
SB9 DrugBefore_NO Parabacteroides 3.829e-04
SB11 DrugBefore_NO Faecalibacterium -1.125e-02
SB16 DrugBefore_YES Faecalibacterium -7.158e-03
SB18 DrugBefore_NO Faecalibacterium -3.502e-01
SB28 DrugBefore_YES Faecalibacterium -1.501e-02
SB29 DrugBefore_YES Faecalibacterium 8.999e-03
SB34 DrugBefore_YES Faecalibacterium 5.444e-03
SB36 DrugBefore_YES Faecalibacterium 2.635e-02
SB39 DrugBefore_YES Faecalibacterium -3.989e-02
SB4 DrugBefore_YES Faecalibacterium 9.151e-03
SB41 DrugBefore_YES Faecalibacterium -2.501e-02
SB43 DrugBefore_YES Faecalibacterium 2.918e-02
SB44 DrugBefore_YES Faecalibacterium -3.242e-01
SB5 DrugBefore_NO Faecalibacterium 1.145e-01
SB9 DrugBefore_NO Faecalibacterium 8.209e-03
SB11 DrugBefore_NO Unclassified_Lachnospiraceae -2.678e-02
SB16 DrugBefore_YES Unclassified_Lachnospiraceae 1.918e-02
SB18 DrugBefore_NO Unclassified_Lachnospiraceae -9.434e-02
SB28 DrugBefore_YES Unclassified_Lachnospiraceae -3.522e-02
SB29 DrugBefore_YES Unclassified_Lachnospiraceae 2.825e-03
SB34 DrugBefore_YES Unclassified_Lachnospiraceae 1.867e-02
SB36 DrugBefore_YES Unclassified_Lachnospiraceae -5.679e-02
SB39 DrugBefore_YES Unclassified_Lachnospiraceae -1.802e-02
SB4 DrugBefore_YES Unclassified_Lachnospiraceae 5.201e-03
SB41 DrugBefore_YES Unclassified_Lachnospiraceae 6.086e-03
SB43 DrugBefore_YES Unclassified_Lachnospiraceae -1.535e-01
SB44 DrugBefore_YES Unclassified_Lachnospiraceae -1.796e-01
SB5 DrugBefore_NO Unclassified_Lachnospiraceae 7.834e-02
SB9 DrugBefore_NO Unclassified_Lachnospiraceae 4.273e-02
SB11 DrugBefore_NO Lactobacillus 0.000e+00
SB16 DrugBefore_YES Lactobacillus -5.567e-05
SB18 DrugBefore_NO Lactobacillus 6.199e-04
SB28 DrugBefore_YES Lactobacillus 0.000e+00
SB29 DrugBefore_YES Lactobacillus 0.000e+00
SB34 DrugBefore_YES Lactobacillus 0.000e+00
SB36 DrugBefore_YES Lactobacillus 0.000e+00
SB39 DrugBefore_YES Lactobacillus 0.000e+00
SB4 DrugBefore_YES Lactobacillus 0.000e+00
SB41 DrugBefore_YES Lactobacillus 0.000e+00
SB43 DrugBefore_YES Lactobacillus -1.018e-03
SB44 DrugBefore_YES Lactobacillus -3.103e-04
SB5 DrugBefore_NO Lactobacillus 1.961e-03
SB9 DrugBefore_NO Lactobacillus 4.491e-03
SB11 DrugBefore_NO Enterococcus 0.000e+00
SB16 DrugBefore_YES Enterococcus 0.000e+00
SB18 DrugBefore_NO Enterococcus 7.126e-02
SB28 DrugBefore_YES Enterococcus 3.934e-04
SB29 DrugBefore_YES Enterococcus -6.612e-01
SB34 DrugBefore_YES Enterococcus -8.525e-05
SB36 DrugBefore_YES Enterococcus 0.000e+00
SB39 DrugBefore_YES Enterococcus 0.000e+00
SB4 DrugBefore_YES Enterococcus -1.777e-04
SB41 DrugBefore_YES Enterococcus 0.000e+00
SB43 DrugBefore_YES Enterococcus -6.788e-04
SB44 DrugBefore_YES Enterococcus 0.000e+00
SB5 DrugBefore_NO Enterococcus 1.089e-04
SB9 DrugBefore_NO Enterococcus 7.573e-04
SB11 DrugBefore_NO Alistipes 2.004e-01
SB16 DrugBefore_YES Alistipes -1.674e-01
SB18 DrugBefore_NO Alistipes 2.480e-04
SB28 DrugBefore_YES Alistipes 0.000e+00
SB29 DrugBefore_YES Alistipes 2.807e-02
SB34 DrugBefore_YES Alistipes -3.394e-02
SB36 DrugBefore_YES Alistipes 2.739e-02
SB39 DrugBefore_YES Alistipes -4.407e-03
SB4 DrugBefore_YES Alistipes 0.000e+00
SB41 DrugBefore_YES Alistipes 1.169e-02
SB43 DrugBefore_YES Alistipes 1.058e-02
SB44 DrugBefore_YES Alistipes 4.393e-03
SB5 DrugBefore_NO Alistipes -6.851e-04
SB9 DrugBefore_NO Alistipes 0.000e+00
SB11 DrugBefore_NO Lachnospiracea_incertae_sedis -2.726e-02
SB16 DrugBefore_YES Lachnospiracea_incertae_sedis -3.510e-03
SB18 DrugBefore_NO Lachnospiracea_incertae_sedis -5.343e-02
SB28 DrugBefore_YES Lachnospiracea_incertae_sedis -5.969e-02
SB29 DrugBefore_YES Lachnospiracea_incertae_sedis 3.240e-03
SB34 DrugBefore_YES Lachnospiracea_incertae_sedis -1.643e-02
SB36 DrugBefore_YES Lachnospiracea_incertae_sedis -2.874e-02
SB39 DrugBefore_YES Lachnospiracea_incertae_sedis -5.941e-03
SB4 DrugBefore_YES Lachnospiracea_incertae_sedis 6.921e-04
SB41 DrugBefore_YES Lachnospiracea_incertae_sedis -5.300e-03
SB43 DrugBefore_YES Lachnospiracea_incertae_sedis -1.407e-01
SB44 DrugBefore_YES Lachnospiracea_incertae_sedis -1.205e-01
SB5 DrugBefore_NO Lachnospiracea_incertae_sedis 4.237e-03
SB9 DrugBefore_NO Lachnospiracea_incertae_sedis -8.762e-03
SB11 DrugBefore_NO Clostridium_XI 3.446e-02
SB16 DrugBefore_YES Clostridium_XI -2.186e-03
SB18 DrugBefore_NO Clostridium_XI -1.666e-02
SB28 DrugBefore_YES Clostridium_XI 3.236e-02
SB29 DrugBefore_YES Clostridium_XI 1.800e-03
SB34 DrugBefore_YES Clostridium_XI 5.249e-04
SB36 DrugBefore_YES Clostridium_XI 2.747e-03
SB39 DrugBefore_YES Clostridium_XI 6.716e-03
SB4 DrugBefore_YES Clostridium_XI -1.096e-04
SB41 DrugBefore_YES Clostridium_XI -1.082e-03
SB43 DrugBefore_YES Clostridium_XI -1.461e-01
SB44 DrugBefore_YES Clostridium_XI 2.282e-03
SB5 DrugBefore_NO Clostridium_XI 2.127e-01
SB9 DrugBefore_NO Clostridium_XI 3.483e-02
SB11 DrugBefore_NO Blautia -7.727e-02
SB16 DrugBefore_YES Blautia -1.041e-03
SB18 DrugBefore_NO Blautia -3.563e-02
SB28 DrugBefore_YES Blautia -3.264e-04
SB29 DrugBefore_YES Blautia 1.080e-03
SB34 DrugBefore_YES Blautia 2.461e-02
SB36 DrugBefore_YES Blautia -1.504e-02
SB39 DrugBefore_YES Blautia -8.720e-03
SB4 DrugBefore_YES Blautia 6.934e-03
SB41 DrugBefore_YES Blautia -6.399e-03
SB43 DrugBefore_YES Blautia -1.208e-01
SB44 DrugBefore_YES Blautia -2.787e-03
SB5 DrugBefore_NO Blautia 4.988e-02
SB9 DrugBefore_NO Blautia 4.537e-02
SB11 DrugBefore_NO Erysipelotrichaceae_incertae_sedis -4.125e-04
SB16 DrugBefore_YES Erysipelotrichaceae_incertae_sedis 3.883e-03
SB18 DrugBefore_NO Erysipelotrichaceae_incertae_sedis -1.880e-03
SB28 DrugBefore_YES Erysipelotrichaceae_incertae_sedis 1.416e-03
SB29 DrugBefore_YES Erysipelotrichaceae_incertae_sedis -6.221e-03
SB34 DrugBefore_YES Erysipelotrichaceae_incertae_sedis 7.007e-04
SB36 DrugBefore_YES Erysipelotrichaceae_incertae_sedis -2.877e-04
SB39 DrugBefore_YES Erysipelotrichaceae_incertae_sedis 6.482e-03
SB4 DrugBefore_YES Erysipelotrichaceae_incertae_sedis 3.714e-03
SB41 DrugBefore_YES Erysipelotrichaceae_incertae_sedis -6.165e-04
SB43 DrugBefore_YES Erysipelotrichaceae_incertae_sedis 1.521e-03
SB44 DrugBefore_YES Erysipelotrichaceae_incertae_sedis 7.523e-04
SB5 DrugBefore_NO Erysipelotrichaceae_incertae_sedis 3.499e-02
SB9 DrugBefore_NO Erysipelotrichaceae_incertae_sedis 3.765e-01
SB11 DrugBefore_NO Roseburia -2.166e-02
SB16 DrugBefore_YES Roseburia 6.445e-05
SB18 DrugBefore_NO Roseburia -9.067e-02
SB28 DrugBefore_YES Roseburia -4.079e-02
SB29 DrugBefore_YES Roseburia 3.052e-04
SB34 DrugBefore_YES Roseburia -2.465e-03
SB36 DrugBefore_YES Roseburia -4.243e-03
SB39 DrugBefore_YES Roseburia -1.960e-02
SB4 DrugBefore_YES Roseburia 1.751e-03
SB41 DrugBefore_YES Roseburia 3.222e-03
SB43 DrugBefore_YES Roseburia -1.403e-02
SB44 DrugBefore_YES Roseburia -4.611e-02
SB5 DrugBefore_NO Roseburia 1.556e-02
SB9 DrugBefore_NO Roseburia 1.548e-02
SB11 DrugBefore_NO Escherichia_Shigella 4.464e-04
SB16 DrugBefore_YES Escherichia_Shigella 1.448e-02
SB18 DrugBefore_NO Escherichia_Shigella 0.000e+00
SB28 DrugBefore_YES Escherichia_Shigella 1.738e-01
SB29 DrugBefore_YES Escherichia_Shigella 0.000e+00
SB34 DrugBefore_YES Escherichia_Shigella -8.525e-05
SB36 DrugBefore_YES Escherichia_Shigella 0.000e+00
SB39 DrugBefore_YES Escherichia_Shigella 0.000e+00
SB4 DrugBefore_YES Escherichia_Shigella 0.000e+00
SB41 DrugBefore_YES Escherichia_Shigella -3.863e-05
SB43 DrugBefore_YES Escherichia_Shigella 0.000e+00
SB44 DrugBefore_YES Escherichia_Shigella 1.098e-03
SB5 DrugBefore_NO Escherichia_Shigella 1.282e-01
SB9 DrugBefore_NO Escherichia_Shigella 2.165e-03
SB11 DrugBefore_NO Unclassified_Clostridiales -8.878e-03
SB16 DrugBefore_YES Unclassified_Clostridiales 6.334e-03
SB18 DrugBefore_NO Unclassified_Clostridiales -6.188e-03
SB28 DrugBefore_YES Unclassified_Clostridiales -1.171e-03

(1.4.1.3.4.2.4.2.1.1.1) Widget 264. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Drug.Before.Diet. Click to see HTML widget file in full window: ./1.4.1.3.4.2.4.2.1.1.1-32346b3cf2bDynamic.Pivot.Table.html

(1.4.1.3.4.2.4.2.1.1.1) Widget 265. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Drug.Before.Diet. Click to see HTML widget file in full window: ./1.4.1.3.4.2.4.2.1.1.1-3236cfb1506Dynamic.Pivot.Table.html

(1.4.1.3.4.2.4.2.1.1.1) Table 253. Summary table. Data grouped by Drug.Before.Diet. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.4.1.3.4.2.4.2.1.1.1-3235dbfdac6.1.4.1.3.4.2.4.2.1.1.csv

feature Drug.Before.Diet mean sd median incidence
Lachnospiracea_incertae_sedis DrugBefore_NO -2.131e-02 2.502e-02 -1.801e-02 0.25
Lachnospiracea_incertae_sedis DrugBefore_YES -3.768e-02 5.254e-02 -1.118e-02 0.20
Unclassified_Bacteria DrugBefore_NO 2.203e-03 2.757e-03 2.265e-03 0.75
Unclassified_Bacteria DrugBefore_YES 1.884e-03 4.153e-03 1.292e-03 0.60
Erysipelotrichaceae_incertae_sedis DrugBefore_NO 1.023e-01 1.836e-01 1.729e-02 0.50
Erysipelotrichaceae_incertae_sedis DrugBefore_YES 1.134e-03 3.376e-03 1.084e-03 0.70
Clostridium_XlVa DrugBefore_NO 7.913e-03 1.463e-02 2.635e-03 0.50
Clostridium_XlVa DrugBefore_YES 1.898e-03 2.707e-03 2.047e-03 0.80
Clostridium_XVIII DrugBefore_NO 3.254e-05 8.909e-03 5.979e-04 0.75
Clostridium_XVIII DrugBefore_YES 2.171e-03 3.518e-03 4.772e-04 0.70
Bacteroides DrugBefore_NO 1.390e-01 2.813e-01 1.643e-02 0.75
Bacteroides DrugBefore_YES 1.510e-01 2.768e-01 6.254e-02 0.70
Clostridium_XI DrugBefore_NO 6.632e-02 1.005e-01 3.464e-02 0.75
Clostridium_XI DrugBefore_YES -1.030e-02 4.876e-02 1.162e-03 0.60
Roseburia DrugBefore_NO -2.032e-02 5.007e-02 -3.090e-03 0.50
Roseburia DrugBefore_YES -1.219e-02 1.802e-02 -3.354e-03 0.40
Clostridium_IV DrugBefore_NO -8.035e-04 1.871e-03 -4.999e-05 0.50
Clostridium_IV DrugBefore_YES 1.863e-03 3.434e-03 3.103e-04 0.60
Unclassified_Clostridiales DrugBefore_NO -2.144e-03 1.581e-02 -7.533e-03 0.25
Unclassified_Clostridiales DrugBefore_YES -4.573e-03 1.171e-02 -4.331e-04 0.50
Unclassified_Lachnospiraceae DrugBefore_NO -1.331e-05 7.655e-02 7.973e-03 0.50
Unclassified_Lachnospiraceae DrugBefore_YES -3.912e-02 7.157e-02 -7.599e-03 0.50
Prevotella DrugBefore_NO -3.044e-01 3.567e-01 -3.008e-01 0.25
Prevotella DrugBefore_YES 1.249e-02 1.574e-01 -5.138e-05 0.40
Flavonifractor DrugBefore_NO 7.722e-04 5.071e-03 1.281e-03 0.75
Flavonifractor DrugBefore_YES 7.164e-05 3.469e-03 5.549e-04 0.60
Blautia DrugBefore_NO -4.414e-03 6.247e-02 4.868e-03 0.50
Blautia DrugBefore_YES -1.225e-02 3.958e-02 -1.914e-03 0.30
Faecalibacterium DrugBefore_NO -5.970e-02 2.014e-01 -1.518e-03 0.50
Faecalibacterium DrugBefore_YES -3.322e-02 1.045e-01 -8.567e-04 0.50
Escherichia_Shigella DrugBefore_NO 3.271e-02 6.368e-02 1.306e-03 0.75
Escherichia_Shigella DrugBefore_YES 1.892e-02 5.460e-02 0.000e+00 0.30
Unclassified_Bacteroidales DrugBefore_NO -2.024e-02 4.456e-02 -1.250e-02 0.25
Unclassified_Bacteroidales DrugBefore_YES 7.899e-03 1.945e-02 1.174e-03 0.70
Unclassified_Ruminococcaceae DrugBefore_NO -9.541e-03 1.337e-02 -9.914e-03 0.25
Unclassified_Ruminococcaceae DrugBefore_YES 5.324e-03 7.846e-03 5.123e-03 0.70
Ruminococcus DrugBefore_NO -1.023e-02 1.334e-02 -7.571e-03 0.25
Ruminococcus DrugBefore_YES 4.363e-03 1.407e-02 6.942e-05 0.50
Unclassified_Firmicutes DrugBefore_NO -1.047e-02 1.110e-02 -9.506e-03 0.25
Unclassified_Firmicutes DrugBefore_YES 3.867e-04 3.882e-03 5.868e-04 0.60
Dorea DrugBefore_NO 1.002e-02 2.151e-02 1.807e-03 0.50
Dorea DrugBefore_YES 8.655e-04 4.056e-03 -1.719e-04 0.40
Clostridium_sensu_stricto DrugBefore_NO 7.453e-03 1.381e-02 9.260e-04 0.50
Clostridium_sensu_stricto DrugBefore_YES 1.803e-03 1.023e-02 0.000e+00 0.40
Parabacteroides DrugBefore_NO -2.580e-02 5.141e-02 -3.407e-04 0.25
Parabacteroides DrugBefore_YES -6.672e-03 6.053e-02 0.000e+00 0.40
Veillonella DrugBefore_NO -7.279e-03 2.598e-02 -1.101e-03 0.25
Veillonella DrugBefore_YES -6.552e-03 2.162e-02 0.000e+00 0.30
Streptococcus DrugBefore_NO 8.042e-03 1.007e-02 7.556e-03 0.50
Streptococcus DrugBefore_YES -7.779e-04 3.537e-03 -2.569e-05 0.40
Alistipes DrugBefore_NO 4.998e-02 1.003e-01 1.240e-04 0.50
Alistipes DrugBefore_YES -1.236e-02 5.723e-02 2.197e-03 0.50
Gemmiger DrugBefore_NO -1.922e-03 4.536e-03 9.139e-05 0.50
Gemmiger DrugBefore_YES -9.231e-04 2.519e-03 0.000e+00 0.20
Enterococcus DrugBefore_NO 1.803e-02 3.549e-02 4.331e-04 0.75
Enterococcus DrugBefore_YES -6.618e-02 2.091e-01 0.000e+00 0.10
Sutterella DrugBefore_NO -4.864e-03 6.883e-03 -2.509e-03 0.25
Sutterella DrugBefore_YES 4.193e-03 1.324e-02 0.000e+00 0.40
Turicibacter DrugBefore_NO 3.041e-03 5.181e-03 7.081e-04 0.50
Turicibacter DrugBefore_YES -3.498e-03 1.069e-02 0.000e+00 0.30
Lactobacillus DrugBefore_NO 1.768e-03 1.991e-03 1.290e-03 0.75
Lactobacillus DrugBefore_YES -1.384e-04 3.240e-04 0.000e+00 0.00
Unclassified_Enterobacteriaceae DrugBefore_NO 2.668e-03 4.844e-03 3.786e-04 0.50
Unclassified_Enterobacteriaceae DrugBefore_YES 3.559e-03 1.369e-02 0.000e+00 0.20
Akkermansia DrugBefore_NO 6.866e-03 1.373e-02 0.000e+00 0.25
Akkermansia DrugBefore_YES 1.708e-02 5.526e-02 0.000e+00 0.20
Unclassified_Lactobacillales DrugBefore_NO 3.631e-02 7.255e-02 5.447e-05 0.50
Unclassified_Lactobacillales DrugBefore_YES -2.819e-05 7.176e-05 0.000e+00 0.00
Megamonas DrugBefore_NO 2.724e-05 5.447e-05 0.000e+00 0.25
Megamonas DrugBefore_YES 0.000e+00 0.000e+00 0.000e+00 0.00
Odoribacter DrugBefore_NO 9.627e-04 7.006e-03 0.000e+00 0.25
Odoribacter DrugBefore_YES 1.390e-03 4.848e-03 0.000e+00 0.10
Unclassified_Burkholderiales DrugBefore_NO 0.000e+00 0.000e+00 0.000e+00 0.00
Unclassified_Burkholderiales DrugBefore_YES -4.832e-03 1.532e-02 0.000e+00 0.10
Parasutterella DrugBefore_NO -3.485e-03 6.970e-03 0.000e+00 0.00
Parasutterella DrugBefore_YES 1.663e-04 5.259e-04 0.000e+00 0.10

(1.4.1.3.4.2.4.2.1.1.1) Figure 781. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar_stacked plot. Image file: plots/323772e23aa.svg.

(1.4.1.3.4.2.4.2.1.1.1) Figure 782. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample mean) plot. Image file: plots/323122621df.svg.

(1.4.1.3.4.2.4.2.1.1.1) Figure 783. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/3235584cfcc.svg.

(1.4.1.3.4.2.4.2.1.1.1) Figure 784. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/323339d76b9.svg.

(1.4.1.3.4.2.4.2.1.2) Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.3.4.2.4.2.1.2.1) Figure 785. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample mean) plot. Image file: plots/32323c42db6.svg.

(1.4.1.3.4.2.4.2.1.2.1) Figure 786. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/323363c50dc.svg.

(1.4.1.3.4.2.4.2.1.2.1) Figure 787. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3236fd8ef7d.svg.

(1.4.1.3.4.2.4.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.4.1.3.4.2.4.2.2.1) Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.4.1.3.4.2.4.2.2.1.1) Figure 788. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample mean) plot. Image file: plots/3231a553ca6.svg.

(1.4.1.3.4.2.4.2.2.1.1) Figure 789. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/32332e603c3.svg.

(1.4.1.3.4.2.4.2.2.1.1) Figure 790. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3233f536f8d.svg.

(1.4.1.3.4.2.4.2.2.2) Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.4.1.3.4.2.4.2.2.2.1) Figure 791. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. bar (sample mean) plot. Image file: plots/3231926d9b.svg.

(1.4.1.3.4.2.4.2.2.2.1) Figure 792. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. violin plot. Image file: plots/32335e088db.svg.

(1.4.1.3.4.2.4.2.2.2.1) Figure 793. Abundance difference between paired samples. Samples are paired according to attribute SubjectID, resulting in 14 pairs. When fold change or difference is computed, this is done as 'before.diet by after.diet'. Data grouped by Drug.Before.Diet. Sorting order of features is GeneSelector paired test ranking. boxplot plot. Image file: plots/3231d3f11df.svg.

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